Rafał Powalski

Maciej Sypetkowski, Joanna Krawczyk, Łukasz Smoliński et al.

Interpreting transcriptomic data is one of the most common analytical tasks in modern biology. Yet most current models either consume expression profiles without producing natural-language biological explanations, or reason in language without direct access to quantitative omics measurements. We introduce OmicsLM, a multimodal LLM that connects quantitative omics profiles with natural-language biological tasks. OmicsLM represents each transcriptomic profile as a compact continuous representation within the LLM context. This interface preserves quantitative expression signal while allowing natural-language instructions, explicit gene mentions, and multiple interleaved biological samples to be processed together in one model context. We train OmicsLM on more than 5.5 million instruction-following examples spanning over 70 task types, combining continuous transcriptomic inputs, experimental data rendered through diverse language templates, and free-text biological knowledge and question-answering data. This mixture covers cell type annotation, perturbation prediction, clinical prediction, pathway reasoning, and open-ended biological question answering. Existing benchmarks evaluate either profile-level prediction or text-only biological QA, leaving language-guided, multi-sample reasoning over real expression profiles unmeasured. To close this gap, we introduce GEO-OmicsQA, a benchmark for multi-sample biological question answering built from real Gene Expression Omnibus (GEO) studies. We demonstrate that OmicsLM can use expression profiles directly and perform comparably to specialized omics models on profile-level tasks, while outperforming both omics-specialized models and general LLMs on language-guided biological reasoning over expression data.

Remigiusz Kinas, Joanna Krawczyk, Rafał Powalski et al.

Translational medicine turns underspecified development goals into evidence synthesis that must combine literature, trials, patents, and quantitative multi-omics analysis while preserving identifiers, uncertainty, and retrievable provenance. General-purpose foundation models and off-the-shelf tool-augmented or multi-agent systems are not built for this: they tend to produce single-shot answers or run open-endedly, and fall short on the auditable, scenario-specific workflows that heterogeneous biomedical sources demand. This paper introduces Ingenix BioResearcher, a scenario-guided multi-agent system that maps queries to versioned research playbooks, delegates to specialized subagents over 30+ tools and machine-learning endpoints, mixes structured database access with sandboxed code for genome-scale analyses, and applies claim-level multi-model reconciliation before editorial assembly. We evaluate BioResearcher across unit-level capabilities, open-ended biomedical reasoning, and end-to-end clinical discovery. It leads evaluated baselines on 109 single-step tests (83.49% pass rate; 0.892 average score), achieves strong biomedical benchmark performance (89.33% on BixBench-Verified-50 and the top 0.758 mean score on BaisBench Scientific Discovery), and leads on a 30-query clinical end-to-end benchmark with the highest positive hit rate (74.7% $\pm$ 3.3%) and negative clear rate (96.8% $\pm$ 0.2%). These results show broad, competitive performance across unit-level, open-ended, and end-to-end clinical evaluations.

Rafał Powalski, Bazyli Klockiewicz, Maciej Jaśkowski et al.

Accelerating molecular docking -- the process of predicting how molecules bind to protein targets -- could boost small-molecule drug discovery and revolutionize medicine. Unfortunately, current molecular docking tools are too slow to screen potential drugs against all relevant proteins, which often results in missed drug candidates or unexpected side effects occurring in clinical trials. To address this gap, we introduce RapidDock, an efficient transformer-based model for blind molecular docking. RapidDock achieves at least a $100 \times$ speed advantage over existing methods without compromising accuracy. On the Posebusters and DockGen benchmarks, our method achieves $52.1\%$ and $44.0\%$ success rates ($\text{RMSD}<2$Å), respectively. The average inference time is $0.04$ seconds on a single GPU, highlighting RapidDock's potential for large-scale docking studies. We examine the key features of RapidDock that enable leveraging the transformer architecture for molecular docking, including the use of relative distance embeddings of $3$D structures in attention matrices, pre-training on protein folding, and a custom loss function invariant to molecular symmetries.

Jordy Van Landeghem, Rubén Tito, Łukasz Borchmann et al.

We call on the Document AI (DocAI) community to reevaluate current methodologies and embrace the challenge of creating more practically-oriented benchmarks. Document Understanding Dataset and Evaluation (DUDE) seeks to remediate the halted research progress in understanding visually-rich documents (VRDs). We present a new dataset with novelties related to types of questions, answers, and document layouts based on multi-industry, multi-domain, and multi-page VRDs of various origins, and dates. Moreover, we are pushing the boundaries of current methods by creating multi-task and multi-domain evaluation setups that more accurately simulate real-world situations where powerful generalization and adaptation under low-resource settings are desired. DUDE aims to set a new standard as a more practical, long-standing benchmark for the community, and we hope that it will lead to future extensions and contributions that address real-world challenges. Finally, our work illustrates the importance of finding more efficient ways to model language, images, and layout in DocAI.

Rafał Powalski, Łukasz Borchmann, Dawid Jurkiewicz et al.

We address the challenging problem of Natural Language Comprehension beyond plain-text documents by introducing the TILT neural network architecture which simultaneously learns layout information, visual features, and textual semantics. Contrary to previous approaches, we rely on a decoder capable of unifying a variety of problems involving natural language. The layout is represented as an attention bias and complemented with contextualized visual information, while the core of our model is a pretrained encoder-decoder Transformer. Our novel approach achieves state-of-the-art results in extracting information from documents and answering questions which demand layout understanding (DocVQA, CORD, SROIE). At the same time, we simplify the process by employing an end-to-end model.

Łukasz Garncarek, Rafał Powalski, Tomasz Stanisławek et al.

We introduce a simple new approach to the problem of understanding documents where non-trivial layout influences the local semantics. To this end, we modify the Transformer encoder architecture in a way that allows it to use layout features obtained from an OCR system, without the need to re-learn language semantics from scratch. We only augment the input of the model with the coordinates of token bounding boxes, avoiding, in this way, the use of raw images. This leads to a layout-aware language model which can then be fine-tuned on downstream tasks. The model is evaluated on an end-to-end information extraction task using four publicly available datasets: Kleister NDA, Kleister Charity, SROIE and CORD. We show that our model achieves superior performance on datasets consisting of visually rich documents, while also outperforming the baseline RoBERTa on documents with flat layout (NDA \(F_{1}\) increase from 78.50 to 80.42). Our solution ranked first on the public leaderboard for the Key Information Extraction from the SROIE dataset, improving the SOTA \(F_{1}\)-score from 97.81 to 98.17.